IRES Track I: US-Sweden Clinical Bioinformatics Research Training Program

IRES Track I：美国-瑞典临床生物信息学研究培训项目

• 批准号: 1951792
• 负责人: Mark Chapman
• 金额: $ 29.92万
• 依托单位: University of San Diego
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1951792&HistoricalAwards=false
• 关键词: IRES; Track; US; Sweden; Clinical

The publication of the first human genome in 2001 transformed biomedical research. Since then, an explosion of new technologies has required engineers and computer scientists to invent computational methods to analyze and interpret complex biological datasets. The efforts to develop these computational methods created the new field of bioinformatics. Over the past two decades, bioinformatics methods have aided in the development of diagnostics, therapies, and predictive models of many disease, including cancer, diabetes, and heart disease. The continual development of bioinformatics tools to analyze and interpret biological data is critical to advancing data-driven healthcare. Therefore, the future of healthcare depends on developing educational programs to train young scientists as bioinformaticians. Given this need, this IRES site aims to train 6 undergraduate students per year from primarily undergraduate institutions (PUIs) in Southern California to conduct 10 weeks of supervised bioinformatics research at the Science for Life Laboratory (SciLifeLab) in Stockholm, Sweden. SciLifeLab is a consortium of researchers from Sweden’s top universities: the Karolinska Institute, Stockholm University, The Royal Institute of Technology, and Uppsala University, and is a global leader in using genomic data and bioinformatics to advance human health. In addition to educating the next generation of bioinformaticians, a goal of this program is to train a diverse cohort of researchers that become globally-engaged scientists. To achieve this, this IRES program will focus on recruiting students from PUIs who are traditionally under-represented in engineering. Recruitment will focus on PUIs because these students typically have fewer research opportunities at their home institutions and will greatly benefit from this program. To ensure student success, extensive predeparture training will provide a foundation in bioinformatics and prepare students for living abroad. Furthermore, upon returning from Sweden, students will have the opportunity to present their work at the annual Biomedical Engineering Society meeting and will be encouraged to maintain an active virtual collaboration with their research group at SciLifeLab. The diverse array of projects which the IRES students will be involved in are at the forefront of clinical bioinformatics. Specifically, students will be involved in developing computational methods to better understand kidney, breast and liver cancers, abdominal aortic aneurysms, skeletal muscle adaptation to exercise and the spatial organization of chromosomes in the nucleus. All of these projects involve analyzing sequencing data from clinically relevant (i.e. human) samples to broaden our knowledge of fundamental biology and the diagnosis/treatment of human disease. Additionally, this work advances engineering knowledge by developing new computational methods useful to the field of bioinformatics. Not only does this program seek to provide exciting research opportunities for undergraduate students, but it also gives these students a chance to live abroad and experience a different culture. Exposure to different cultural backgrounds and ways of thinking can influence student global perspectives and challenge preconceived notions about the world. Moreover, working with researchers from different cultural backgrounds will give students tools to communicate in our ever-globalizing society. This program will likely be the first time abroad for many of the student participants, so the experience will be both professionally and personally formative.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

2001年第一个人类基因组的出版改变了生物医学研究。从那时起，新技术的爆炸激增要求工程师和计算机科学家发明计算方法来分析和解释复杂的生物学数据集。开发这些计算方法的努力创造了新的生物信息学领域。在过去的二十年中，生物信息学方法有助于诊断，疗法和预测模型的发展，包括癌症，糖尿病和心脏病。分析和解释生物学数据的生物信息学工具的持续开发对于推进数据驱动的医疗保健至关重要。因此，医疗保健的未来取决于制定教育计划，以培训年轻科学家作为生物信息学家。鉴于此需求，此IRES网站旨在每年从南加州的小学本科机构（PUI）培训6名本科生，以在瑞典斯德哥尔摩的科学生命实验室（SCILIFELAB）进行10周监督生物信息学研究。 Scilifelab是瑞典顶级大学的研究人员的联盟：卡罗林斯卡研究所，斯德哥尔摩大学，皇家理工学院和乌普萨拉大学，并且是使用基因组数据和生物信息学来促进人类健康的全球领导者。除了教育下一代生物信息学家外，该计划的目标是培训一群成为全球科学家的研究人员。为了实现这一目标，该IRES计划将着重于招募来自PUI的学生，这些PUI传统上代表性不足。招聘将重点放在PUI上，因为这些学生通常在其家庭机构中拥有更少的研究机会，并且将从该计划中受益匪浅。为了确保学生的成功，广泛的前部培训将为生物信息学提供基础，并为学生做好准备。此外，从瑞典返回后，学生将有机会在年度生物医学工程协会会议上介绍他们的作品，并将鼓励与Scilifelab的研究小组保持积极的虚拟合作。 IRES学生将参与的潜水员阵列位于临床生物信息学的最前沿。特别是，学生将参与开发计算方法，以更好地了解肾脏，乳腺癌和肝癌，腹部主动脉动脉瘤，骨骼肌适应运动以及核心中染色体的空间组织。所有这些项目都涉及分析从临床相关（即人类）样本的测序数据，以扩大我们对基本生物学的了解和人类疾病的诊断/治疗。此外，这项工作通过开发对生物信息学领域有用的新计算方法来提高工程知识。该计划不仅试图为本科生提供令人兴奋的研究机会，而且还使这些学生有机会在国外生活和体验不同的文化。接触不同的文化背景和思维方式可以影响学生全球的观点，并挑战有关世界的先入为主的笔记。此外，与来自不同文化背景的研究人员合作将为学生提供在我们不断变化的社会中进行交流的工具。该计划可能是许多学生参与者的首次出国，因此该经验将是专业和个人形成的。该奖项反映了NSF的法定任务，并使用基金会的知识分子优点和更广泛的影响评估审查标准，被认为是珍贵的支持。

项目成果

US-Sweden Bioinformatics NSF-IRES Year 1: Program Development and Initial Lessons Learned

美国-瑞典生物信息学 NSF-IRES 第一年：项目开发和初步经验教训

• 发表时间: 2022
• 期刊: 2022 American Society for Engineering Education Annual Conference and Exposition
• 作者: Chapman, Mark A

US-Sweden Bioinformatics IRES: Investigating Engineering Students’ Attitudes and Perspectives Throughout a 10-week International Research Program

美国-瑞典生物信息学 IRES：在为期 10 周的国际研究项目中调查工程专业学生的态度和观点

• 发表时间: 2022
• 期刊: 2022 American Society for Engineering Education Annual Conference & Exposition
• 作者: Chapman, Mark A;Forbes, Marissa H.
• 通讯作者: Forbes, Marissa H.

Work in Progress: Development of a Training Program to Prepare Students for an Immersive Bioinformatics Summer Research Experience

正在进行的工作：制定培训计划，为学生提供沉浸式生物信息学夏季研究体验

• 发表时间: 2021
• 期刊: 2021 American Society for Engineering Education Virtual Annual Conference
• 作者: Chapman, MA

Discovery of drug targets and therapeutic agents based on drug repositioning to treat lung adenocarcinoma

• DOI: 10.1016/j.biopha.2023.114486
• 发表时间: 2023-03-10
• 期刊: BIOMEDICINE & PHARMACOTHERAPY
• 影响因子: 7.5
• 作者: Graves, Occam Kelly;Kim, Woonghee;Li, Xiangyu
• 通讯作者: Li, Xiangyu

US-Sweden Bioinformatics IRES Year 2: Improving Student Preparedness

美国-瑞典生物信息学 IRES 第 2 年：提高学生的准备程度

• 发表时间: 2023
• 期刊: 2023 ASEE Annual Conference & Exposition
• 作者: Chapman, Mark A.